title: Histone ChIP-seq from prostate gland (ENCLB513OOQ)

description:
https://www.encodeproject.org/experiments/ENCSR153NDQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR153NDQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR559IPI
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB513OOQ
fragmentation methods: none
size range: 200-600

value: prostate gland


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB029TMK)

status: Public on Nov 01 2019

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR188HXK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188HXK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB029TMK
fragmentation methods: sonication (generic)
size range: 200-600

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

tag: antibody

value: esophagus muscularis mucosa

value: tissue

tag: description

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 37 year

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_G8

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

library_source: transcriptomic

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

molecule: total RNA

organism: Mus musculus

source_name: Oprm1-Cre nucleus striatum

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain

tag: genotype

tag: treatment

value: untreated


title: Histone ChIP-seq from Peyer's patch (ENCLB857CJL)

description:
https://www.encodeproject.org/experiments/ENCSR667SCY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR667SCY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB857CJL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) Peyer's patch tissue

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

tag: source

value: Kristin Ardlie

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: HEKPAR4plusA

city: London

first: Jamie

middle: M

last: Kramer

state: Ontario

address: 1151 Richmond St.

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

description: rRNA-depleted total RNA

data_processing:
Basecalls performed using RTA v2
RNA-Seq reads were trimmed using Prinseq-lite 0.20.4 quality aware trimming
Reads were aligned to the H. sapiens genome using STAR 2.5.3a
Count tables were generated using HT-Seq Count v0.7.1 to count reads to genic features
Genome_build: Homo sapiens CRCh release 38
Supplementary_files_format_and_content: processed data files are raw count tables in .txt format.

source_name: HEK-293 cells

growth_protocol: Cells were maintained in DMEM with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% sodium pyruvate, and 600 μg/mL geneticin.

extract_protocol:
Qiagen RNeasy mini kit
ScriptSeq complete kit

treatment_protocol: See "SAMPLES" section

value: WT expressing PAR4+YFP

value: Treated with 30μM AYPGKF-NH2


title: Histone ChIP-seq from spleen (ENCLB316TDZ)

description:
https://www.encodeproject.org/experiments/ENCSR091IRL/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR091IRL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316TDZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) spleen tissue

extract_protocol: not provided

value: spleen

value: ENCBS511RRL at ENCODE; https://www.encodeproject.org/ENCBS511RRL/


title: Nucleus Oprm1-Cre:H2BG Mu_G15


title: Nucleus Oprm1-Cre:H2BG Mu_G6


title: HEKPAR4B

description: rRNA-depleted total RNA

value: Control treatment


title: Nucleus Oprm1-Cre:H2BG Mu_G4


title: Histone ChIP-seq from sigmoid colon (ENCLB362PSW)

description:
https://www.encodeproject.org/experiments/ENCSR654KVJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR654KVJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB362PSW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) sigmoid colon tissue

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Histone ChIP-seq from sigmoid colon (ENCLB805HUI)

description:
https://www.encodeproject.org/experiments/ENCSR654KVJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR654KVJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB805HUI
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult

value: 37 year

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_G3

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_G1


title: Nucleus Oprm1-Cre:H2BG Mu_F24


title: Histone ChIP-seq from Peyer's patch (ENCLB338WQE)

description:
https://www.encodeproject.org/experiments/ENCSR667SCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR667SCY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338WQE
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: S_Rep3

city: LOS ANGELES

first: Pinghui

last: Feng

department: Section of Infection and Immunity

institute: Herman Ostrow School of Dentistry, University of Southern California

description: S phase synchronized HCT116 Colorectal Cancer Cells

data_processing:
Illumina NextSeq 500 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into HISAT2 v2.1.0 for alignment into SAM files. SAM files are coverted into BAM files using Samtools v1.9.0
BAM files were imported into the StringTIe v1.3.6, and RPKM counts were calculated using R package Ballgown.
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated values files include FPKM values for each Sample

source_name: Colorectal cancer cells: HCT116

growth_protocol: Reconstituted' HCT116 cells were grown in DMEM/Hi-Glucose containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml), puromycin (1ng/ml), Hygromycin (200ug/ml);  cell cycle synchronized HCT116 cells were grown in DMEM/Hi-Glucose containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the KAPA RNA-Seq library kit.
1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina adaptors prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x75 paired end flow cell.

treatment_protocol: HCT116 cells depleted of endogenous RelA (by stably expressing shRNA target 3'UTR of RelA) were 'reconstituted' with RelA-WT, RelA-DD or RelA-64A by lentivirus-mediated transduction; cell cycle synchronized HCT116 cells were arrested in S phase by double Thymidine block method and G1 phase by Lovastatin. Cells were harvested 1 h after release from arrest and total RNA was extracted for library construction.

tag: cell line


title: Nucleus Oprm1-Cre:H2BG Mu_F23


title: Control ChIP-seq from esophagus squamous epithelium (ENCLB771LGW)

description:
https://www.encodeproject.org/experiments/ENCSR644XSS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR644XSS
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB771LGW
size range: 200-600

source_name: Homo sapiens male adult (54 years) esophagus squamous epithelium tissue

value: Control

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: 54 year

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS143WXN at ENCODE; https://www.encodeproject.org/ENCBS143WXN/


title: S_Rep2


title: Nucleus Oprm1-Cre:H2BG Mu_F22


title: HEKPAR4plusB

description: rRNA-depleted total RNA

value: WT expressing PAR4+YFP

value: Treated with 30μM AYPGKF-NH2


title: Nucleus Oprm1-Cre:H2BG Mu_G7


title: Nucleus Oprm1-Cre:H2BG Mu_F21


title: Histone ChIP-seq from tibial nerve (ENCLB790ADM)

description:
https://www.encodeproject.org/experiments/ENCSR639JPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639JPM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790ADM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial nerve tissue

value: tibial nerve

value: tissue

value: EnTEX:Nerve - Tibial

value: male

value: ENCBS647STW at ENCODE; https://www.encodeproject.org/ENCBS647STW/


title: S_Rep1


title: Histone ChIP-seq from tibial nerve (ENCLB171ABE)

description:
https://www.encodeproject.org/experiments/ENCSR639JPM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR639JPM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR329HFV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB171ABE
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: 37 year

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_F20

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_F19


title: Nucleus Oprm1-Cre:H2BG Mu_G5


title: Nucleus Oprm1-Cre:H2BG Mu_F18


title: G1_Rep2

description: G1 phase synchronized HCT116 Colorectal Cancer Cells


title: Nucleus Oprm1-Cre:H2BG Mu_F17


title: HEKPAR4A

description: rRNA-depleted total RNA

value: Control treatment


title: Histone ChIP-seq from Peyer's patch (ENCLB705GKZ)

description:
https://www.encodeproject.org/experiments/ENCSR632SLJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR632SLJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705GKZ
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Control ChIP-seq from esophagus squamous epithelium (ENCLB728OEF)

description:
https://www.encodeproject.org/experiments/ENCSR644XSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR644XSS
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB728OEF
size range: 200-600

value: Control

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: 54 year

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS143WXN at ENCODE; https://www.encodeproject.org/ENCBS143WXN/


title: Nucleus Oprm1-Cre:H2BG Mu_G2


title: G1_Rep1


title: Nucleus Oprm1-Cre:H2BG Mu_F13


title: Nucleus Oprm1-Cre:H2BG Mu_F12


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB815GOI)

description:
https://www.encodeproject.org/experiments/ENCSR153AXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR153AXQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815GOI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) esophagus squamous epithelium tissue

value: tissue

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: male

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: KD_Rep1

description: RelA mutants 'reconstituted' HCT116 cell line, no treatment


title: KD_Rep2


title: Nucleus Oprm1-Cre:H2BG Mu_F9

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_F11


title: Nucleus Oprm1-Cre:H2BG Mu_F10


title: Histone ChIP-seq from tibial artery (ENCLB747YVN)

description:
https://www.encodeproject.org/experiments/ENCSR626BAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR626BAM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB747YVN
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens male adult (37 years) tibial artery tissue

value: tibial artery

value: EnTEX:Artery - Tibial

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_F8


title: 64A_Rep2


title: G1_Rep3


title: Nucleus Oprm1-Cre:H2BG Mu_F7


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB825XMI)

description:
https://www.encodeproject.org/experiments/ENCSR621MTP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR621MTP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB825XMI
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS884JOD at ENCODE; https://www.encodeproject.org/ENCBS884JOD/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: 64A_Rep1


title: Nucleus Oprm1-Cre:H2BG Mu_F16

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: Histone ChIP-seq from tibial artery (ENCLB461AUO)

description:
https://www.encodeproject.org/experiments/ENCSR626BAM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR626BAM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB461AUO
fragmentation methods: none
size range: 200-600

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_F5


title: Histone ChIP-seq from Peyer's patch (ENCLB892CYA)

description:
https://www.encodeproject.org/experiments/ENCSR632SLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR632SLJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB892CYA
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Nucleus Oprm1-Cre:H2BG Mu_F15


title: Nucleus Oprm1-Cre:H2BG Mu_F4


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB156JJI)

description:
https://www.encodeproject.org/experiments/ENCSR621MTP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR621MTP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR147KFH
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB156JJI
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male


title: Nucleus Oprm1-Cre:H2BG Mu_F2

value: untreated


title: DD_Rep1


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB207RNH)

description:
https://www.encodeproject.org/experiments/ENCSR153AXQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR153AXQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB207RNH
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Nucleus Oprm1-Cre:H2BG Mu_F6


title: Nucleus Oprm1-Cre:H2BG Mu_F3


title: Histone ChIP-seq from breast epithelium (ENCLB456BYO)

description:
https://www.encodeproject.org/experiments/ENCSR134LLK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR134LLK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB456BYO
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) breast epithelium tissue

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: adult

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: Nucleus Oprm1-Cre:H2BG Mu_E24


title: WT_Rep2


title: Histone ChIP-seq from breast epithelium (ENCLB260YHQ)

description:
https://www.encodeproject.org/experiments/ENCSR134LLK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR134LLK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB260YHQ
fragmentation methods: none
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_E23


title: Nucleus Oprm1-Cre:H2BG Mu_F14


title: WT_Rep1


title: Nucleus Oprm1-Cre:H2BG Mu_E22


title: Nucleus Oprm1-Cre:H2BG Mu_E21


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB305ZFI)

description:
https://www.encodeproject.org/experiments/ENCSR600TOW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR600TOW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305ZFI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: Nucleus Oprm1-Cre:H2BG Mu_E20

value: untreated


title: Das_pol2_rep2

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% FBS and Penicillin streptomycin, incubated at 37°C in 5% CO2

extract_protocol:
Sonicated and clarified lysate was incubated with ChIP-seq antibodies on magnetic beads to immunoprecipitate corresponding protein-DNA complexs
Libraries were prepared using NEBNext Ultra II DNA library Prep Kit for Illumina E7645S with NEBNext Multiplex Oligos for Illumina (Index Primer Set 1) E7335S

treatment_protocol: Cells were treated with 10µM Dasatinib, or DMSO for the control samples

value: Dasatinib

tag: chip antibody

value: Ms mAb RNA polymerase II to CTD repeat YSPTSPS (8WG16) Abcam:ab817


title: Das_pol2_rep1


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB285PSI)

description:
https://www.encodeproject.org/experiments/ENCSR600TOW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR600TOW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB285PSI
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB369HWK)

description:
https://www.encodeproject.org/experiments/ENCSR134KZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR134KZX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369HWK
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_E19


title: Nucleus Oprm1-Cre:H2BG Mu_E17


title: Nucleus Oprm1-Cre:H2BG Mu_E18


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB430XUH)

description:
https://www.encodeproject.org/experiments/ENCSR134KZX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR134KZX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB430XUH
fragmentation methods: sonication (generic)
size range: 200-600


title: Das_input_rep2

value: None (Input DNA)


title: Nucleus Oprm1-Cre:H2BG Mu_E16


title: Das_input_rep1


title: Nucleus Oprm1-Cre:H2BG Mu_E15


title: Histone ChIP-seq from upper lobe of left lung (ENCLB801ROU)

description:
https://www.encodeproject.org/experiments/ENCSR595MTV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR595MTV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB801ROU
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: adult

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: Nucleus Oprm1-Cre:H2BG Mu_F1


title: Nucleus Oprm1-Cre:H2BG Mu_E14


title: Nucleus Oprm1-Cre:H2BG Mu_E13


title: Nucleus Oprm1-Cre:H2BG Mu_E12


title: Histone ChIP-seq from upper lobe of left lung (ENCLB648KAF)

description:
https://www.encodeproject.org/experiments/ENCSR595MTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR595MTV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB648KAF
fragmentation methods: sonication (generic)
size range: 200-600


title: ctrl_pol2_rep1

value: DMSO control


title: Nucleus Oprm1-Cre:H2BG Mu_E10


title: Nucleus Oprm1-Cre:H2BG Mu_E11


title: Control ChIP-seq from sigmoid colon (ENCLB386TAT)

description:
https://www.encodeproject.org/experiments/ENCSR099RQB/
***************
biological replicate number: 3
technical replicate number: 2
description:
experiment encode accession: ENCSR099RQB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB386TAT
size range: 200-600

value: Control

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: Bradley Bernstein, Broad

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Nucleus Oprm1-Cre:H2BG Mu_E9


title: Nucleus Oprm1-Cre:H2BG Mu_E8


title: Control ChIP-seq from sigmoid colon (ENCLB878RWJ)

description:
https://www.encodeproject.org/experiments/ENCSR099RQB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR099RQB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB878RWJ
size range: 200-600

value: 37 year

value: Kristin Ardlie

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_E7

value: untreated


title: Control ChIP-seq from sigmoid colon (ENCLB919JXO)

description:
https://www.encodeproject.org/experiments/ENCSR099RQB/
***************
biological replicate number: 3
technical replicate number: 4
description:
experiment encode accession: ENCSR099RQB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919JXO
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_E6


title: Nucleus Oprm1-Cre:H2BG Mu_E5


title: MOLM13_empty_YKL_2

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
X62
MOLM13_empty_DMSO_YKL_DESeq2_Normalized_expression_values.tabular

data_processing:
Sequencing reads were mapped into reference human genome hg19 or mm10 using HISAT2
Reads for protein coding genes were counted using FeatureCounts
Normalized and differentially expressed genes were analyzed using DESeq2
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: tabular, normalized RPKM

molecule: polyA RNA

source_name: actue myeloid luekemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout, or treated with DMSO or YKL-05-099 for 2 hrs

value: MOLM-13 cell harboring empty vector

tag: time point

value: 2 hr

tag: agent


title: Control ChIP-seq from sigmoid colon (ENCLB224THP)

description:
https://www.encodeproject.org/experiments/ENCSR099RQB/
***************
biological replicate number: 3
technical replicate number: 3
description:
experiment encode accession: ENCSR099RQB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB224THP
size range: 200-600

value: tissue

value: male


title: ctrl_pol2_rep2

value: Ms mAb RNA polymerase II to CTD repeat YSPTSPS (8WG16) Abcam:ab817


title: Nucleus Oprm1-Cre:H2BG Mu_E3

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt


title: MOLM13_empty_YKL_1

description:
X41
MOLM13_empty_DMSO_YKL_DESeq2_Normalized_expression_values.tabular


title: Nucleus Oprm1-Cre:H2BG Mu_E2


title: Histone ChIP-seq from spleen (ENCLB763YCM)

description:
https://www.encodeproject.org/experiments/ENCSR091IRL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR091IRL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763YCM
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: adult

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Nucleus Oprm1-Cre:H2BG Mu_D24


title: Nucleus Oprm1-Cre:H2BG Mu_D23


title: MOLM13_empty_DMSO_2

description:
X108
MOLM13_empty_DMSO_YKL_DESeq2_Normalized_expression_values.tabular

value: 0.1percent DMSO


title: Histone ChIP-seq from spleen (ENCLB462VQN)

description:
https://www.encodeproject.org/experiments/ENCSR091IRL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091IRL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB462VQN
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_E1


title: MOLM13_empty_DMSO_1

description:
X39
MOLM13_empty_DMSO_YKL_DESeq2_Normalized_expression_values.tabular


title: Nucleus Oprm1-Cre:H2BG Mu_D22


title: Histone ChIP-seq from breast epithelium (ENCLB123SQH)

description:
https://www.encodeproject.org/experiments/ENCSR568QQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR568QQU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB123SQH
fragmentation methods: sonication (generic)
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: DD_Rep2

description: RelA mutants 'reconstituted' HCT116 cell line, no treatment


title: H3K27ac_MOLM13_SIK3TQ_YKL

data_processing:
Sequencing reads were mapped into reference human genome hg19 using Bowtie2
Peakcalling was done using MACS2 FDR cut off 5% with broad peak option for H3K27ac
The H3K27ac peaks were merged with corresponding control ChIP-seq using BEDtools
Normalized tag count was calculated using Bamliquidator package
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were prepared using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, ChIP DNA was end-repaired, 3’-adenylated, and then ligated with indexed adaptor. These DNA was size selected (200-400 bp) via agarose gel electrophoresis, and PCR amplified. Final products were purified using AMPure XP beads.

treatment_protocol: Cells were treated with DMSO or 250 nM YKL-05-099 for 2 hrs

tag: genotype/variation

value: expressing SIK3T142Q

value: 2 hr treatment of 250 nM YKL-05-099

value: H3K27ac (abcam ab4729)


title: Nucleus Oprm1-Cre:H2BG Mu_D20

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_D21


title: Nucleus Oprm1-Cre:H2BG Mu_D19


title: Histone ChIP-seq from breast epithelium (ENCLB331ZOM)

description:
https://www.encodeproject.org/experiments/ENCSR568QQU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR568QQU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB331ZOM
fragmentation methods: none
size range: 200-600

tag: antibody

value: tissue

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: ctrl_input_rep1

value: DMSO control

value: None (Input DNA)


title: Nucleus Oprm1-Cre:H2BG Mu_D18


title: H3K27ac_MOLM13_SIK3TQ

value: 2 hr treatment of 0.1 percent DMSO


title: Nucleus Oprm1-Cre:H2BG Mu_E4


title: Control ChIP-seq from prostate gland (ENCLB256UDP)

description:
https://www.encodeproject.org/experiments/ENCSR559IPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR559IPI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB256UDP
size range: 200-600

source_name: Homo sapiens male adult (37 years) prostate gland tissue

value: Control

value: prostate gland

tag: description

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: male

value: adult

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS985DZK at ENCODE; https://www.encodeproject.org/ENCBS985DZK/


title: Control ChIP-seq from prostate gland (ENCLB495AMT)

description:
https://www.encodeproject.org/experiments/ENCSR559IPI/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR559IPI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB495AMT
size range: 200-600

tag: biosample encode accession

value: ENCBS866WWM at ENCODE; https://www.encodeproject.org/ENCBS866WWM/


title: Nucleus Oprm1-Cre:H2BG Mu_D14


title: Nucleus Oprm1-Cre:H2BG Mu_D17


title: H3K27ac_MOLM13_empty_YKL

value: harboring empty vector

value: 2 hr treatment of 250 nM YKL-05-099

value: H3K27ac (abcam ab4729)


title: Nucleus Oprm1-Cre:H2BG Mu_D16

value: untreated


title: Control ChIP-seq from prostate gland (ENCLB907XXF)

description:
https://www.encodeproject.org/experiments/ENCSR559IPI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR559IPI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB907XXF
size range: 200-600

value: tissue

tag: Sex

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_D15


title: H3K27ac_MOLM13_empty vector

value: 2 hr treatment of 0.1 percent DMSO


title: ctrl_input_rep2

value: DMSO control

value: None (Input DNA)


title: Nucleus Oprm1-Cre:H2BG Mu_D12


title: Nucleus Oprm1-Cre:H2BG Mu_D13


title: Input_MOLM13_SIK3TQ_YKL

value: expressing SIK3T142Q


title: Input_MOLM13_SIK3TQ


title: Nucleus Oprm1-Cre:H2BG Mu_D11


title: Control ChIP-seq from prostate gland (ENCLB097OIL)

description:
https://www.encodeproject.org/experiments/ENCSR559IPI/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR559IPI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB097OIL
size range: 200-600

value: Control

value: prostate gland

value: EnTEX:Prostate updated Feb 2019 with updated term name and ID from DCC.

value: male

tag: dev stage


title: Control ChIP-seq from prostate gland (ENCLB037HFU)

description:
https://www.encodeproject.org/experiments/ENCSR559IPI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR559IPI
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB037HFU
size range: 200-600

value: adult

tag: age

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Nucleus Oprm1-Cre:H2BG Mu_D9


title: Nucleus Oprm1-Cre:H2BG Mu_D10


title: Nucleus Oprm1-Cre:H2BG Mu_D8


title: Nucleus Oprm1-Cre:H2BG Mu_D7


title: Input_MOLM13_empty_YKL

value: harboring empty vector

value: 2 hr treatment of 250 nM YKL-05-099


title: Input_MOLM13_empty vector


title: Nucleus Oprm1-Cre:H2BG Mu_D6

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_D5


title: Histone ChIP-seq from spleen (ENCLB538DEO)

description:
https://www.encodeproject.org/experiments/ENCSR556QXD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR556QXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538DEO
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: tissue

tag: lab

value: ENCBS486GAC at ENCODE; https://www.encodeproject.org/ENCBS486GAC/


title: Histone ChIP-seq from spleen (ENCLB088FGU)

description:
https://www.encodeproject.org/experiments/ENCSR556QXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR556QXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR889RIF
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB088FGU
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie

tag: link


title: Nucleus Oprm1-Cre:H2BG Mu_D4

tag: background strain


title: Histone ChIP-seq from breast epithelium (ENCLB996GPC)

description:
https://www.encodeproject.org/experiments/ENCSR081OTO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR081OTO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB996GPC
fragmentation methods: none
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: ENCBS444JDU at ENCODE; https://www.encodeproject.org/ENCBS444JDU/


title: Nucleus Oprm1-Cre:H2BG Mu_D3

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

tag: genotype


title: WT Input DNA-IP

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

description: Input DNA-IP

data_processing:
Immunoprecipitation of UV damaged DNA: Sequences were mapped (input and IP) onto the Arabidopsis nuclear genome (TAIR10) using Bowtie 1.1.2 (-v2 –m1). Both CPD and 6,4 PP enriched regions were determined using MACS2 (version 2.1).
WGBS: Mapping on the arabidopsis genome (TAIR10) was performed using Bsmap/methratio.py (Bsmapz version) using default options. Upon mapping, the methylation levels were calculated with methratio.py. Differentially Methylated Regions (DMRs) between untreated and treated plants of the same genotype were determined according Daccord et al. (2017) considering 200 bp sliding-windows with an overlap of 50 bp (sliding-window-pipeline). DMRs were identified using the difference between identical windows and upon filtering. Consecutive windows exhibiting the same methylation change (gain or loss) were joined and methylation level recalculated. DMRs were called for a DNA methylation difference (p<0.05 according Wilcoxon signed-rank test), within the same genotype, higher or equal than 0.4 for CG, 0.2 for CHG and 0.1 for CHH methylation contexts.
Small RNA seq: Reads were aligned and mapped onto the Arabidopsis genome (TAIR10) using Bowtie (version 1.2.1.1; parameters: -y -e 50 -n 0 -a --best --strata –nomaqround). Upon conversion with samtools (version 1.5), reads overlapping with either the UV-damaged loci or the DMRs (50% overlap) were calculated with intersectBed (BEDtools version 2.27.1). The read counts are divided by the “per million” scaling factor (RPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: txt or bed files

organism: Arabidopsis thaliana

source_name: Col 0

growth_protocol: in vitro

extract_protocol:
Genomic DNA was extracted immediately upon UV-C exposure (time point 0) and 24h upon UV-C exposure using the Plant DNA Extraction kit (Qiagen). Small RNAs were prepared from untreated and UV-C treated plants (time points 0 and 24h) using the Tri-Reagent (Sigma)
library preparation and sequencing by Illumina Hi-Seq (FASTERIS, Switzerland)

tag: ecotype

value: Col 0

value: 18 days in vitro

tag: tissue

value: leaves

value: Wild type


title: ago1 photolesions: DNA-IP antibody anti-6,4 PP (CAC-NM-DND-002, Cosmobio)

source_name: Morel et al., 2002 EMBO J


title: Nucleus Oprm1-Cre:H2BG Mu_C24

source_name: Oprm1-Cre nucleus striatum

tag: treatment


title: Histone ChIP-seq from breast epithelium (ENCLB775RMO)

description:
https://www.encodeproject.org/experiments/ENCSR081OTO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR081OTO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR980TBV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB775RMO
fragmentation methods: none
size range: 200-600

value: adult

tag: source


title: TF ChIP-seq from tibial artery (ENCLB021PKO)

description:
https://www.encodeproject.org/experiments/ENCSR079YAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR079YAP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB021PKO
fragmentation methods: none
size range: 200-600

value: CTCF

value: tibial artery

value: EnTEX:Artery - Tibial

value: male

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Nucleus Oprm1-Cre:H2BG Mu_D1

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_C23


title: Nucleus Oprm1-Cre:H2BG Mu_D2


title: Nucleus Oprm1-Cre:H2BG Mu_C22


title: Nucleus Oprm1-Cre:H2BG Mu_C21


title: ago1 photolesions: DNA-IP antibody anti-CPD (CAC-NM-DND-001, Cosmobio)


title: ago1 DMR: WGBS time point 24h UV-C

description: WGBS time point 24h UV-C


title: ago1 DMR: WGBS time point 0

description: WGBS time point 0


title: Nucleus Oprm1-Cre:H2BG Mu_C20


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB246GZR)

description:
https://www.encodeproject.org/experiments/ENCSR079NLY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR079NLY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB246GZR
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa updated Feb 2019 with updated term name and ID from DCC.

value: Bradley Bernstein, Broad

value: ENCBS608MZC at ENCODE; https://www.encodeproject.org/ENCBS608MZC/


title: Nucleus Oprm1-Cre:H2BG Mu_C19


title: Small RNA seq ago1 24h: time point 24h UV-C

description: small RNA time point 24h UV-C

value: Col 0

value: 18 days in vitro


title: Nucleus Oprm1-Cre:H2BG Mu_C18


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB803GPX)

description:
https://www.encodeproject.org/experiments/ENCSR079NLY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR079NLY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR156WTZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB803GPX
fragmentation methods: sonication (generic)
size range: 200-600


title: Nucleus Oprm1-Cre:H2BG Mu_C17


title: Histone ChIP-seq from upper lobe of left lung (ENCLB733UNX)

description:
https://www.encodeproject.org/experiments/ENCSR074WIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074WIB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB733UNX
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: Kristin Ardlie

value: ENCBS943JOF at ENCODE; https://www.encodeproject.org/ENCBS943JOF/


title: Nucleus Oprm1-Cre:H2BG Mu_C16


title: dcl4 photolesions: DNA-IP antibody anti-6,4 PP (CAC-NM-DND-002, Cosmobio)

value: leaves


title: Nucleus Oprm1-Cre:H2BG Mu_C15


title: Histone ChIP-seq from upper lobe of left lung (ENCLB200JLW)

description:
https://www.encodeproject.org/experiments/ENCSR074WIB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR074WIB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR746QZL
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200JLW
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: Nucleus Oprm1-Cre:H2BG Mu_C14


title: dcl4 photolesions: DNA-IP antibody anti-CPD (CAC-NM-DND-001, Cosmobio)


title: Nucleus Oprm1-Cre:H2BG Mu_C13


title: Nucleus Oprm1-Cre:H2BG Mu_C10


title: Histone ChIP-seq from Peyer's patch (ENCLB708THL)

description:
https://www.encodeproject.org/experiments/ENCSR063BPD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR063BPD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB708THL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) Peyer's patch tissue

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum updated Feb 2019 with updated term name and ID from DCC.

value: male

value: ENCBS388XLV at ENCODE; https://www.encodeproject.org/ENCBS388XLV/


title: Nucleus Oprm1-Cre:H2BG Mu_C11

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_C12


title: Nucleus Oprm1-Cre:H2BG Mu_C8


title: TF ChIP-seq from tibial artery (ENCLB731OSO)

description:
https://www.encodeproject.org/experiments/ENCSR079YAP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR079YAP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR807FIZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB731OSO
fragmentation methods: none
size range: 200-600

value: CTCF

value: tibial artery

value: EnTEX:Artery - Tibial

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS452GMG at ENCODE; https://www.encodeproject.org/ENCBS452GMG/


title: Histone ChIP-seq from Peyer's patch (ENCLB671VIN)

description:
https://www.encodeproject.org/experiments/ENCSR063BPD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063BPD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR708OCZ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB671VIN
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad


title: Nucleus Oprm1-Cre:H2BG Mu_C7


title: dcl4 DMR: WGBS time point 0

description: WGBS time point 0

value: Col 0

value: 18 days in vitro


title: dcl4 DMR: WGBS time point 24h UV-C

description: WGBS time point 24h UV-C

value: leaves


title: Small RNA seq dcl4 24h: time point 24h UV-C

description: small RNA time point 24h UV-C


title: Nucleus Oprm1-Cre:H2BG Mu_C6


title: Nucleus Oprm1-Cre:H2BG Mu_C9


title: Histone ChIP-seq from sigmoid colon (ENCLB616NMJ)

description:
https://www.encodeproject.org/experiments/ENCSR043RXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR043RXI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB616NMJ
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: adult

value: Kristin Ardlie

value: ENCBS365ZJJ at ENCODE; https://www.encodeproject.org/ENCBS365ZJJ/


title: Small RNA seq ago1 0: time point 0

description: small RNA time point 0


title: Small RNA seq dcl4 0: time point 0

description: small RNA time point 0


title: Nucleus Oprm1-Cre:H2BG Mu_C4

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_C3


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB316MWH)

description:
https://www.encodeproject.org/experiments/ENCSR037GFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR037GFN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316MWH
fragmentation methods: sonication (generic)
size range: 200-600

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction updated Feb 2019 with updated term name and ID from DCC.

value: male

value: ENCBS727XQL at ENCODE; https://www.encodeproject.org/ENCBS727XQL/


title: Nucleus Oprm1-Cre:H2BG Mu_C5


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB536SDH)

description:
https://www.encodeproject.org/experiments/ENCSR037GFN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR037GFN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR343GIV
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB536SDH
fragmentation methods: sonication (generic)
size range: 200-600

value: 37 year

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ddb2 photolesions: DNA-IP antibody anti-6,4 PP (CAC-NM-DND-002, Cosmobio)

source_name: Schalk et al., 2016 Plant Cell


title: Nucleus Oprm1-Cre:H2BG Mu_C2


title: Histone ChIP-seq from sigmoid colon (ENCLB385PBC)

description:
https://www.encodeproject.org/experiments/ENCSR043RXI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR043RXI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR099RQB
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385PBC
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: ddb2 photolesions: DNA-IP antibody anti-CPD (CAC-NM-DND-001, Cosmobio)


title: Nucleus Oprm1-Cre:H2BG Mu_B23


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB537GQK)

description:
https://www.encodeproject.org/experiments/ENCSR012KZW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR012KZW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR644XSS
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB537GQK
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: 54 year

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS143WXN at ENCODE; https://www.encodeproject.org/ENCBS143WXN/


title: Nucleus Oprm1-Cre:H2BG Mu_C1


title: Nucleus Oprm1-Cre:H2BG Mu_B24


title: ddb2 DMR: WGBS time point 24h UV-C

description: WGBS time point 24h UV-C

value: Col 0

value: 18 days in vitro

value: leaves


title: Nucleus Oprm1-Cre:H2BG Mu_B22

value: untreated


title: ddb2 DMR: WGBS time point 0

description: WGBS time point 0


title: Nucleus Oprm1-Cre:H2BG Mu_B20


title: Small RNA seq ddb2 24h: time point 24h UV-C

description: small RNA time point 24h UV-C


title: TEAD4-ChIP-3

city: Washington

first: Max

middle: Harley

last: Kushner

state: DC

address: 3970 Reservoir Rd NW, NRB E311

department: Oncology

institute: Georgetown University

data_processing:
Data was aligned to indexed Hg38 by BWA MEM
Output SAM files were converted to BAM, Sorted, and de-duplicated with SAMTOOLS
Peaks were called with MACS2 against the input file as a control (Sample 7)
Replicates were merged using Bedtools if peaks were present in at least 2/3 samples. Bedtools -intersect was used to detect overlap in pairwise comparison, then resulting overlaps were merged with Bedtools -everything.
Genome_build: GRCh38
Supplementary_files_format_and_content: AIB1_Interesect_Everything.bed contains peaks present in at least 2/3 triplicate AIB1 ChIP samples
Supplementary_files_format_and_content: TEAD4_Interesect_Everything.bed contains peaks present in at least 2/3 triplicate TEAD4 ChIP samples

source_name: Mammary Epthelial Cells

growth_protocol: MCF10A cell lines were maintained in DMEM:F12 (Invitrogen, Carlsbad, CA) with 5% horse serum, 20ng/ml EGF, 0.5mg/ml Hydrocortisone, 100ng/ml Cholera Toxin, and 10mg/mL Insulin. All cell lines were grown at 37C with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and Antibody-DNA complexes were isolated with antibody.
Libraries were prepared according to ActiveMotif's Low Cell ChIP-seq Kit instructions.

value: Normal Immortalized MCF10A Mammary Epithelial Cells

tag: passage


title: Input


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB249QJV)

description:
https://www.encodeproject.org/experiments/ENCSR012KZW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR012KZW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR644XSS
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249QJV
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: Kristin Ardlie


title: Nucleus Oprm1-Cre:H2BG Mu_B18


title: Nucleus Oprm1-Cre:H2BG Mu_B21


title: Nucleus Oprm1-Cre:H2BG Mu_B19


title: Nucleus Oprm1-Cre:H2BG Mu_B17


title: Small RNA seq ddb2 0: time point 0

description: small RNA time point 0


title: uvr3 phrI photolesions: DNA-IP antibody anti-6,4 PP (CAC-NM-DND-002, Cosmobio)

source_name: WiscDsLox334H05 and WiscDsLox466C12

value: uvr3 phrI


title: Nucleus Oprm1-Cre:H2BG Mu_B16


title: TEAD4-ChIP-2


title: TEAD4-ChIP-1


title: Nucleus Oprm1-Cre:H2BG Mu_B15


title: Nucleus Oprm1-Cre:H2BG Mu_B14


title: AIB1-ChIP-3

value: CST 2126, Lot 4


title: uvr3 phrI DMR: WGBS time point 24h UV-C

description: WGBS time point 24h UV-C


title: uvr3 phrI photolesions: DNA-IP antibody anti-CPD (CAC-NM-DND-001, Cosmobio)


title: Nucleus Oprm1-Cre:H2BG Mu_B11


title: Nucleus Oprm1-Cre:H2BG Mu_B10


title: AIB1-ChIP-2


title: Nucleus Oprm1-Cre:H2BG Mu_B9


title: uvr3 phrI DMR: WGBS time point 0

description: WGBS time point 0


title: Nucleus Oprm1-Cre:H2BG Mu_B8


title: AIB1-ChIP-1


title: Nucleus Oprm1-Cre:H2BG Mu_B7


title: Small RNA seq uvr3 phrI 24h: time point 24h UV-C

description: small RNA time point 24h UV-C


title: Nucleus Oprm1-Cre:H2BG Mu_B6


title: Nucleus Oprm1-Cre:H2BG Mu_B5


title: Small RNA seq uvr3 phrI 0: time point 0

description: small RNA time point 0


title: WT photolesions: DNA-IP antibody anti-6,4 PP (CAC-NM-DND-002, Cosmobio)

value: Wild type


title: Nucleus Oprm1-Cre:H2BG Mu_B4


title: Nucleus Oprm1-Cre:H2BG Mu_B2


title: Nucleus Oprm1-Cre:H2BG Mu_B3


title: Nucleus Oprm1-Cre:H2BG Mu_B12


title: Nucleus Oprm1-Cre:H2BG Mu_B1


title: Nucleus Oprm1-Cre:H2BG Mu_A24


title: WT photolesions: DNA-IP antibody anti-CPD (CAC-NM-DND-001, Cosmobio)


title: WT DMR: WGBS time point 24h UV-C

description: WGBS time point 24h UV-C


title: Nucleus Oprm1-Cre:H2BG Mu_A23


title: MCF-7_E2(+)_IgG

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was performed using tophat 2.1.0.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to facilitate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: Summary of RPKM for RefSeq genes

source_name: ER-positive breast cancer cells

growth_protocol: MCF-7 cells were maintained in phenol red-free Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% charcoal stripped-FBS. MDA-MB-231 cells were maintained in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were lysed and protein-RNA complexes were precipitated with PSF or NONO antibody, or IgG.
SureSelect RNAXT RNA Target Enrichment for Illumina Multiplexed Sequencing (Agilent) was used for library construction according to the manufacturer's protocol.

treatment_protocol: MCF-7 cells were treated with 10 nM E2 or control vehicle (ethanol) for 12 hours.

tag: cell line

tag: cell type

value: ER-positive breast cancer cells

tag: rip antiobdy

value: IgG

value: 10 nM E2


title: MCF-7_E2(+)_PSF

value: PSF (Sigma WH0006421M2)


title: MCF-7_E2(-)_NONO

value: Vehicle


title: MCF-7_E2(+)_Input


title: WT DMR: WGBS time point 0

description: WGBS time point 0

tag: genotype/variation


title: Nucleus Oprm1-Cre:H2BG Mu_A21


title: Nucleus Oprm1-Cre:H2BG Mu_A20


title: MCF-7_E2(-)_PSF


title: Nucleus Oprm1-Cre:H2BG Mu_A19


title: Small RNA seq WT 24h: time point 24h UV-C

description: small RNA time point 24h UV-C


title: MCF-7_E2(-)_IgG


title: Nucleus Oprm1-Cre:H2BG Mu_A17


title: MCF-7_E2(-)_Input

source_name: ER-negative breast cancer cells

value: ER-negative breast cancer cells


title: Small RNA seq WT 0: time point 0

description: small RNA time point 0


title: Nucleus Oprm1-Cre:H2BG Mu_A16


title: Nucleus Oprm1-Cre:H2BG Mu_A15


title: Nucleus Oprm1-Cre:H2BG Mu_A14


title: Nucleus Oprm1-Cre:H2BG Mu_B13


title: Nucleus Oprm1-Cre:H2BG Mu_A22


title: MDA-MB-231_PSF


title: Nucleus Oprm1-Cre:H2BG Mu_A13


title: Nucleus Oprm1-Cre:H2BG Mu_A11


title: Nucleus Oprm1-Cre:H2BG Mu_A12


title: MDA-MB-231_NONO


title: Nucleus Oprm1-Cre:H2BG Mu_A10


title: Nucleus Oprm1-Cre:H2BG Mu_A9


title: MDA-MB-231_IgG


title: Nucleus Oprm1-Cre:H2BG Mu_A8


title: Nucleus Oprm1-Cre:H2BG Mu_A18


title: MDA-MB-231_Input


title: 11_Hypoxia_siARNT_B

city: Zurich

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

country: Switzerland

institute: ETH Zürich

description: AsPC-1 cells were seeded in 6-well plates in triplicates and transduced with siScramble or siARNT using Lipofectamine RNAiMAX. The next day, cells were split 1:2 and transferred to a hypoxic chamber (1% O2, 24h) or kept under normoxic culture conditions. 48h after transfection, cells were harvested using the Nucleospin® RNA extraction protocol (Machery-Nagel).

data_processing:
Sequencing reads were trimmed using trimmomatic (39) to remove residual Illumina oligonucleotide sequences on the 3’ end of each tag (options: ILLUMINACLIP: TruSeq3-SE.fa:2:30:8 LEADING:25 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The remaining reads were aligned to the GRCh38.p10 human genome assembly using STAR 2.4.2a together with the Genecode v26 gene annotation (default parameters). The search for novel junctions was allowed during the mapping step.
Gene level read counts were generated using the QoRTs software v1.2.42 after excluding reads with multiple alignments (MAPK score less than 255)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Processed gene level counts are tab-delimited raw counts observed with matching ensembl id. Splice event quantification is in a tab delimited format indicating the number of reads identified in the flaking exons as well as the junction reads.

growth_protocol: Standard mammalian cell culture

extract_protocol:
Cells were harvested using the Nucleospin® RNA extraction protocol (Machery-Nagel)
(TruSeq® Illumina mRNA (Poly(A) enrichment) stranded
Sequencing was performed on three lanes (HiSeq, SR125, 250-300 M reads per lane)

tag: o2 status

value: Hypoxic

tag: sirna status

value: siARNT


title: 8_Hypoxia_siControl_B

treatment_protocol: AsPC-1 cells were seeded in 6-well plates in triplicates and transduced with siScramble or siARNT using Lipofectamine RNAiMAX. The next day, cells were split 1:2 and transferred to a hypoxic chamber (1% O2, 24h) or kept under normoxic culture conditions

value: siControl


title: 9_Hypoxia_siControl_C


title: MCF10A-YAPS94A-shAIB1#2-3

data_processing:
Data was aligned to Hg38 by STAR 2.7; Gene Counts were generated with the following specifications: --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode TranscriptomeSAM GeneCounts
Count tables were merged with gawk (10A_Merged_reads, processed data files)
Counts per million were generated with EdgeR 3.8 (CPM_df.tsv, processed data files)
Genome_build: GRCh38
Supplementary_files_format_and_content: CPM_df.tsv is a tab-separated values file containing the Counts Per Million of each sample
10A_Merged_reads is a text file containing merged gene counts reads generated by EdgeR --quantMode GeneCounts commant

extract_protocol:
RNA was isolated from cultured cells, spheres, or tissues using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol and quantified by Nanodrop (Thermo Fisher, Waltham, MA).
RNA-sequencing used TruSeq total RNA with RiboZero Gold library preparation (Illumina, San Diego, CA, USA).


title: MCF-7_E2(+)_NONO


title: 7_Hypoxia_siControl_A


title: 12_Hypoxia_siARNT_C


title: MCF10A-YAPS94A-shAIB1#2-2


title: MCF10A-YAPS94A-shAIB1#2-1


title: 6_Normoxia_siARNT_C

value: Normoxic


title: Nucleus Oprm1-Cre:H2BG Mu_A2

description:
SS2_16_033_Oprm1_counts.txt
SS2_16_striatal_nuclei_counts.txt

value: untreated


title: Nucleus Oprm1-Cre:H2BG Mu_A1


title: Nucleus Oprm1-Cre:H2BG Mu_A7


title: Nucleus Slc32a1-Cre:H2BG Vg_P23

description:
SS2_16_033_Slc32a1_counts.txt
SS2_16_striatal_nuclei_counts.txt

source_name: Slc32a1-Cre nucleus striatum


title: 4_Normoxia_siARNT_A


title: MCF10A-YAPS94A-shAIB1#1-2

value: Normal Immortalized MCF10A Mammary Epithelial Cells


title: Nucleus Slc32a1-Cre:H2BG Vg_P22


title: MCF10A-YAPS94A-shAIB1#1-3


title: Nucleus Slc32a1-Cre:H2BG Vg_P24


title: 10_Hypoxia_siARNT_A


title: 5_Normoxia_siARNT_B


title: Nucleus Oprm1-Cre:H2BG Mu_A5


title: Nucleus Oprm1-Cre:H2BG Mu_A4


title: Nucleus Oprm1-Cre:H2BG Mu_A6


title: 3_Normoxia_siControl_C


title: Nucleus Slc32a1-Cre:H2BG Vg_P20


title: MCF10A-YAPS94A-shAIB1#1-1


title: 2_Normoxia_siControl_B


title: Nucleus Slc32a1-Cre:H2BG Vg_P19


title: Nucleus Oprm1-Cre:H2BG Mu_A3


title: 1_Normoxia_siControl_A


title: MCF10A-YAPS94A-shGFP-2


title: Nucleus Slc32a1-Cre:H2BG Vg_P16


title: Nucleus Slc32a1-Cre:H2BG Vg_P18


title: Nucleus Slc32a1-Cre:H2BG Vg_P21


title: Nucleus Slc32a1-Cre:H2BG Vg_P13


title: MCF10A-YAPS94A-shGFP-1


title: MCF10A-YAP-shAIB1#2-2


title: ZAP-L 144A CLIP Reads Mapped to HIV-1 CG High

city: New York

first: Matthew

middle: A

last: Takata

address: 1230 York Ave

institute: The Rockefeller Univeristy

description:
Processed CLIP Reads, cellular and viral
ZAP_L_144A_CG_High_NL43

data_processing:
Library strategy: PAR-CLIP
The FASTX toolkit was used to process the reads from libraries before mapping. Briefly, reads that contained ambiguous nucleotides, did not contain the 3′ adapter sequence or were shorter than 15nt were discarded. The remaining reads were then separated based on their 5’ barcode sequences and collapsed to generate a set of unique sequences.
Reads were then aligned to the human genome (hg19) or to the HIV-1 genome(NL4-3 and NDK), with up to 2 mismatches allowed using the Bowtie algorithm. In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
BEDTools was used to convert the mapped reads to unique CLIP tags.
Genome_build: hg19, NL4-3 CG-High (GenBank Submission ID: 2254750)
Supplementary_files_format_and_content: fastq

growth_protocol: HEK293T cells stably expressing ZAP-L with an C-terminal HA tag were grown in 15-cm dishes and infected with NL4-3 HIV

extract_protocol:
UV-crosslinked cells were lysed, ZAP-RNA complexes were immunoprecipitatd and RNA was extracted for library construction. Libraries were prepared with sequential ligation of the following primers: 3' adapter: 5'adenylated/TCG TAT GCC GTC TTC TGC TTG-3'dideoxyC / 5' adapters containing the barcodes are as follows: rGUU CAG AGU UCU ACA GUC CGA CGA UC AGUGC rGUU CAG AGU UCU ACA GUC CGA CGA UC GAUGC rGUU CAG AGU UCU ACA GUC CGA CGA UC GUGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC ACGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC UAGGC rGUU CAG AGU UCU ACA GUC CGA CGA UC AUCGC
Once the extracted RNA had the appropriate adaptors ligated, a gene specific primer was used to create and cDNA library. The DNA library was further amplified by PCR and purified on a TBE-Urea gel.

treatment_protocol: For PAR-CLIP, one day following infection and 14 hours before harvesting cell, 100μM 40thiouridine (4SU) was added to the cell culture medium

value: 293T expressing ZAP-L 144A with 3xHA tag

tag: clip antibody

value: mouse anti-HA (Biolegend, Cat#:901502, Lot#:B218907)

tag: viral expression

value: Transfection

tag: virus

value: NL4-3 L (organism:Human immunodeficiency virus 1; strain:NL4-3; genotype:CG High)


title: Nucleus Slc32a1-Cre:H2BG Vg_P12


title: ZAP-L 144Y CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_144Y_CG_High_NL43

value: 293T expressing ZAP-L 144Y with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_P10


title: Nucleus Slc32a1-Cre:H2BG Vg_P11


title: Nucleus Slc32a1-Cre:H2BG Vg_P9


title: ZAP-L 108A CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_108A_CG_High_NL43

value: 293T expressing ZAP-L 108A with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_P8


title: ZAP-L 108F CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_108F_CG_High_NL43

value: 293T expressing ZAP-L 108F with 3xHA tag


title: MCF10A-YAP-shAIB1#2-1


title: ZAP-L 107R CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_107R_CG_High_NL43

value: 293T expressing ZAP-L 107R with 3xHA tag


title: MCF10A-YAPS94A-shGFP-3


title: MCF10A-YAP-shAIB1#1-3


title: Nucleus Slc32a1-Cre:H2BG Vg_P7


title: Nucleus Slc32a1-Cre:H2BG Vg_P17


title: Nucleus Slc32a1-Cre:H2BG Vg_P15


title: ZAP-L 107A CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_107A_CG_High_NL43

value: 293T expressing ZAP-L 107A with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_P3


title: MCF10A-YAP-shAIB1#1-2


title: Nucleus Slc32a1-Cre:H2BG Vg_P5


title: ZAP-L 98F CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_98F_CG_High_NL43

value: 293T expressing ZAP-L 98F with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_P2


title: MCF10A-YAP-shAIB1#2-3


title: Nucleus Slc32a1-Cre:H2BG Vg_P14


title: MCF10A-YAP-shAIB1#1-1


title: Nucleus Slc32a1-Cre:H2BG Vg_P1


title: ZAP-L 98A CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_98A_CG_High_NL43

value: 293T expressing ZAP-L 98A with 3xHA tag


title: MCF10A-YAP-shGFP-3


title: Nucleus Slc32a1-Cre:H2BG Vg_O23


title: Nucleus Slc32a1-Cre:H2BG Vg_O21


title: MCF10A-YAP-shGFP-2


title: ZAP-L 89A CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_89A_CG_High_NL43

value: 293T expressing ZAP-L 89A with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_P6


title: Nucleus Slc32a1-Cre:H2BG Vg_O20


title: Nucleus Slc32a1-Cre:H2BG Vg_O19


title: Nucleus Slc32a1-Cre:H2BG Vg_P4


title: ZAP-L WT CLIP CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_WT_CG_High_NL43

value: 293T expressing ZAP-L WT with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_O18


title: Nucleus Slc32a1-Cre:H2BG Vg_O17


title: Nucleus Slc32a1-Cre:H2BG Vg_O16


title: Subject 1519073 Post

city: Orlando

first: Rick

last: Vega

state: FL

address: 303 E. Princeton

institute: AdventHealth

description: Skeletal muscle biopsy

data_processing:
Reads were mapped using tophat 2.0.1
mRNA quantification and normalization was performed with Partek Genomic Suite 6.6
Differential expression was calculated using Bioconductor DEseq R package as described in Anders S, Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, R106.
Genome_build: hg38

source_name: Vastus lateralis muscle

extract_protocol:
Muscle biopsies were obtained using a Berstrom needle. The biopsy was trimmed of visible adipose tissue and flash frozen in liquid nitrogen. Total RNA was isolated using the RNeasy fibrous tissue kit.
1microgram of total RNA was utilized for library construction using the Illumina Truseq stranded Total RNA library preparation kit.

tag: time point

value: Post

value: Vastus lateralis


title: Nucleus Slc32a1-Cre:H2BG Vg_O15

tag: background strain

value: untreated


title: Nucleus Slc32a1-Cre:H2BG Vg_O12

tag: genotype


title: Subject 1519070 Post

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_O14


title: Nucleus Slc32a1-Cre:H2BG Vg_O24


title: Subject 1519070 Pre

description: Skeletal muscle biopsy

value: Pre


title: Nucleus Slc32a1-Cre:H2BG Vg_O22


title: ZAP-L 89R CLIP Reads Mapped to HIV-1 CG High

description:
Processed CLIP Reads, cellular and viral
ZAP_L_89R_CG_High_NL43

value: 293T expressing ZAP-L 89R with 3xHA tag


title: Nucleus Slc32a1-Cre:H2BG Vg_O9


title: Nucleus Slc32a1-Cre:H2BG Vg_O13


title: Nucleus Slc32a1-Cre:H2BG Vg_O8


title: Subject 1519053 Post

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_O7


title: Subject 1519053 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_O6


title: Adult retinal ganglion cell_rep28 [non-dissociated RGC]

type: RNA

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

description:
cDNA
Gene expression data from a single mouse retinal ganglion cell.

hyb_protocol: Amplified cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using standard Affymetrix protocols at the Genomics facility at the University of Iowa.

scan_protocol: Affymetrix Mouse Genome 430 2.0 arrays were scanned using standard protocols at the Genomics facility at the University of Iowa.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

source_name: Adult retina

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

growth_protocol: Retinas were dissected under IR light (940 nm) and cuts were made along cardinal directions before the retina was mounted, ganglion cell side up, on a 12mm coated glass coverslip. The coverslip was secured to the recording dish and placed on the electrophysiology rig and the retina was superfused with 32°C pre-warmed carbogenated Ames medium.

extract_protocol: Individual ganglion cells were harvested based on their physiological properties using a pulled glass pipette and were expelled into cold lysis buffer. The total single cell RNA was reverse transcribed using Superscript III combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Tissue was illuminated at 950nm for visualization and cell attached recordings were completed using pipettes filled with Ames solution via 2-channel patch-clamp amplifier (MultiClamp 700B, Molecular Devices). To display visual stimuli, a custom-designed light projection device (DLP LightCrafter, Texas Instruments) was employed and experiments relied on blue LED illumination with a peak spectral output at 450nm. Various visual stimuli were projected upon the retina and each RGC’s response was monitored. Single cells were isolated based on their response and immediately placed into cell lysis buffer.

tag: strain/background

value: retina

value: retinal ganglion

tag: age

value: adult

tag: physiological property of rgc

value: On Sustained Non-Alpha


title: Adult retinal ganglion cell_rep27 [non-dissociated RGC]

tag: tissue

value: On Pixel Encoder


title: MCF10A-YAP-shGFP-1

value: Normal Immortalized MCF10A Mammary Epithelial Cells

tag: passage


title: Adult retinal ganglion cell_rep25 [non-dissociated RGC]

value: Suppressed by Contrast


title: Subject 1519073 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_O5

tag: treatment


title: Nucleus Slc32a1-Cre:H2BG Vg_O3


title: Nucleus Slc32a1-Cre:H2BG Vg_O11


title: Subject 1519050 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_O1


title: Adult retinal ganglion cell_rep29 [non-dissociated RGC]

tag: cell type

value: Local Edge Detector


title: Nucleus Slc32a1-Cre:H2BG Vg_O10


title: Adult retinal ganglion cell_rep26 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_O4


title: Subject 1519050 Post

description: Skeletal muscle biopsy


title: Subject 1519049 Post

description: Skeletal muscle biopsy


title: Subject 1519049 Pre

description: Skeletal muscle biopsy


title: Adult retinal ganglion cell_rep23 [non-dissociated RGC]

value: Off High Speed Selective


title: Nucleus Slc32a1-Cre:H2BG Vg_O2


title: Nucleus Slc32a1-Cre:H2BG Vg_N21


title: Adult retinal ganglion cell_rep24 [non-dissociated RGC]

value: Eyewire Cell 4i


title: Adult retinal ganglion cell_rep22 [non-dissociated RGC]

value: Eyewire Cell 6sn


title: Nucleus Slc32a1-Cre:H2BG Vg_N19


title: Nucleus Slc32a1-Cre:H2BG Vg_N18


title: Nucleus Slc32a1-Cre:H2BG Vg_N20


title: Adult retinal ganglion cell_rep20 [non-dissociated RGC]

value: Off Transient Alpha


title: Nucleus Slc32a1-Cre:H2BG Vg_N24


title: Nucleus Slc32a1-Cre:H2BG Vg_N23


title: Adult retinal ganglion cell_rep21 [non-dissociated RGC]

value: Eyewire Cell 6sw


title: Nucleus Slc32a1-Cre:H2BG Vg_N22


title: Nucleus Slc32a1-Cre:H2BG Vg_N16


title: Subject 1519031 Post

description: Skeletal muscle biopsy

value: Post

value: Vastus lateralis


title: Subject 1519031 Pre

description: Skeletal muscle biopsy

value: Pre


title: Subject 1519032 Post

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_N14

value: untreated


title: Nucleus Slc32a1-Cre:H2BG Vg_N17


title: Nucleus Slc32a1-Cre:H2BG Vg_N13


title: Subject 1519032 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_N11


title: Subject 1519015 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_N15


title: Nucleus Slc32a1-Cre:H2BG Vg_N12


title: Subject 1519008 Post

description: Skeletal muscle biopsy


title: Adult retinal ganglion cell_rep18 [non-dissociated RGC]

value: retina

value: Off Sustained Alpha


title: Subject 1519015 Post

description: Skeletal muscle biopsy


title: Adult retinal ganglion cell_rep19 [non-dissociated RGC]

value: retinal ganglion

value: adult


title: Adult retinal ganglion cell_rep17 [non-dissociated RGC]


title: Adult retinal ganglion cell_rep16 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_N10


title: Nucleus Slc32a1-Cre:H2BG Vg_N9


title: Nucleus Slc32a1-Cre:H2BG Vg_N6


title: Nucleus Slc32a1-Cre:H2BG Vg_N8


title: Subject 1519006 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_N3


title: Subject 1519008 Pre

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_N4


title: sgRNA_810

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

data_processing:
Sequenced reads were aligned to the human genome (hg19) using TopHat2
Gene expression counts were calculated using HTseq using based on Ensembl's human gene annotations (v69).
Expression levels were normalized using RPKM and then quantile normalization.
Only genes with at least 20 counts in at least one sample were included.
To avoid fold-change inflation for lowly expressed genes, expression levels below 0.7 RPKM were set to 0.7
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression data matrix (normalized by FPKM followed by quantile norm.)

growth_protocol: MCF-7 cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS (Hyclone), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNA was extracted using TRIsure (Bioline) reagent and following the manufacturers protocol.
RNA-seq samples were processed with TruSeq RNA library prep kit v2 (Illumina)

treatment_protocol: MCF-7 cells were infected with the indicated sgRNAs. After the antibiotic selection was completed, cells were kept in cell culture until they reach 70-80% confluency. Total RNA was extracted using TRIsure (Bioline) reagent and following the manufacturers protocol.

tag: cell line

tag: sgrna


title: Nucleus Slc32a1-Cre:H2BG Vg_N2


title: Nucleus Slc32a1-Cre:H2BG Vg_N5


title: Adult retinal ganglion cell_rep15 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_N1


title: Subject 1519006 Post

description: Skeletal muscle biopsy


title: Nucleus Slc32a1-Cre:H2BG Vg_M24


title: Adult retinal ganglion cell_rep13 [non-dissociated RGC]

value: On Alpha


title: sgRNA_1659


title: Adult retinal ganglion cell_rep12 [non-dissociated RGC]


title: sgRNA_680


title: Adult retinal ganglion cell_rep14 [non-dissociated RGC]


title: Adult retinal ganglion cell_rep11 [non-dissociated RGC]

value: J-RGC


title: Nucleus Slc32a1-Cre:H2BG Vg_N7


title: Nucleus Slc32a1-Cre:H2BG Vg_M23


title: Adult retinal ganglion cell_rep9 [non-dissociated RGC]

value: On Orientation Selective (vertical)


title: Nucleus Slc32a1-Cre:H2BG Vg_M22


title: Nucleus Slc32a1-Cre:H2BG Vg_M19


title: Nucleus Slc32a1-Cre:H2BG Vg_M18


title: control sgRNAs

value: control sgRNAs


title: sgRNA_1118


title: Nucleus Slc32a1-Cre:H2BG Vg_M20


title: sgRNA1830 targeting ERa binding site and serves here as another control

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Sequenced reads were aligned to the human genome (hg19) using bowtie2
Intervals that show transcriptional activity were detected using the dREG tool.
Reads in dREG intervals were counted using HTSeq-count and then normalized using RPM followed by quantile normalization.
To avoid fold-change inflation for lowly expressed intervals, expression levels below 5 RPM were set to 5
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix for TRE regions identified by dREG. Contains raw counts, normalized levels and log2R values relative to the nontargeting control sample

extract_protocol:
GRO-Seq was performed as described before with minor modifications. Briefly, 5x106 nuclei were isolated and incubated 5 min at 30°C with equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.2 µM CTP+32P CTP) for the nuclear run-on. The reaction was stopped and total RNA was extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. RNA was fragmented using fragmentation reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). BrU-labeled RNA was immunoprecipitated with anti-BrU agarose beads (Santa Cruz), washed one time in binding buffer, one time in low salt buffer (0.2X SSPE, 1 mM EDTA, 0.05% Tween-20), one-time high salt buffer (0.25X SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and two times in TET buffer (TE with 0.05% Tween-20). RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and isolated with Trizol LS. After the binding step, BrU-labbeled RNA was treated with tobacco acid pyrophosphatase (TAP, Epicenter) to remove 5’-methyl guanosine cap, followed by T4 polynucleotide kinase (PNK; NEB) to remove 3’-phosphate group. BrU-containing RNA was treated with T4 PNK again at high pH in the presence of ATP to add 5’-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were prepared using TruSeq Small RNA kit (Illumina) following manufacturer’s instructions. Briefly, end-repaired RNA was ligated to RNA 3’ and 5’ adapters, followed by RT-PCR amplification. cDNA was purified using Agencourt AMPure XP (Beckman Coulter) and amplified by PCR for 12 cycles. Finally, amplicons were cleaned and size-selected using Agencourt AMPure XP (Beckman Coulter), quantified in a Bioanalyzer 2100 (Agilent)


title: Nucleus Slc32a1-Cre:H2BG Vg_M21

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.


title: Nucleus Slc32a1-Cre:H2BG Vg_M16


title: Nucleus Slc32a1-Cre:H2BG Vg_M17


title: Nucleus Slc32a1-Cre:H2BG Vg_M14


title: Nucleus Slc32a1-Cre:H2BG Vg_M15


title: Adult retinal ganglion cell_rep8 [non-dissociated RGC]

value: On-Off Direction Selective


title: Adult retinal ganglion cell_rep7 [non-dissociated RGC]


title: sgRNA1118 targeting CTCF binding site involved in the regulation of the expression of PREX1

description: nascent RNA


title: Nucleus Slc32a1-Cre:H2BG Vg_M13


title: Nucleus Slc32a1-Cre:H2BG Vg_M12


title: Adult retinal ganglion cell_rep6 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_M11


title: control sgRNA

description: nascent RNA

value: Control


title: Adult retinal ganglion cell_rep4 [non-dissociated RGC]

value: On Direction Selective


title: Adult retinal ganglion cell_rep5 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_M9


title: CDLS3-3-MEGs; rep 3

city: Philadelphia

first: Jason

middle: Adam

last: Mills

state: PA

address: 422 Curie Blvd

department: Ophthalmology

institute: The University of Pennsylvania

data_processing:
Align pair-ended reads to reference genome using STAR (version 2.5.1b),  in a 2-pass mode.
The first pass mapped reads to known splice junctions in reference transcriptome (Illumina iGenome) during alignment while allowing for detection of novel junction sites.
Junction sites detected from multiple samples by the first pass were collected, combined and filtered.
The second pass re-aligned reads to the reference genome and transcriptome, plus the novel junction sites detected by the first pass.
Aligned reads were mapped to known genes. Only reads with both ends uniquely mapped to a gene were assigned to that gene to get its read count. Read counts of 3 technical replicates were combined.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: Tab-delimited text file inclduing an integer matrix of gene-level read counts.

source_name: Megakaryocytes (MEGs)

growth_protocol: Megakaryocyte cells were generated as previosly published (Mills JA et al. 2013, Blood).  Megakarycoytes were generated in SFD + TPO + SCF + ascorbic acid media at 37C in 5% CO2 and expanded for 5 days before collection and analysis.

extract_protocol:
Samples were collected and total RNA was isolated using Trizol reagent then collected on Purelink RNA isolation column with DNASE treatment
RNA-seq libraries were prepared with Illumina TruSeq RiboZero Sample Prep kits.  Samples sequenced on a HiSeq 2500 (Illumina), using the paired end protocol with 125 bp read length to obtain three technical sequencing replicates per sample, each individual had three techincal replicates

value: iPSC-derived megakaryocytes

tag: Stage

value: Day 12 post-induction

value: NIPBL+/-


title: Nucleus Slc32a1-Cre:H2BG Vg_M10

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene


title: Nucleus Slc32a1-Cre:H2BG Vg_M8


title: CDLS3-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_M5


title: Nucleus Slc32a1-Cre:H2BG Vg_M6


title: Nucleus Slc32a1-Cre:H2BG Vg_M7


title: Nucleus Slc32a1-Cre:H2BG Vg_M3


title: Nucleus Slc32a1-Cre:H2BG Vg_M4


title: CDLS3-1-MEGs; rep 1


title: CDLS2-3-MEGs; rep 3


title: CDLS2-2-MEGs; rep 2


title: Adult retinal ganglion cell_rep3 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L24


title: Nucleus Slc32a1-Cre:H2BG Vg_M2


title: Adult retinal ganglion cell_rep2 [non-dissociated RGC]


title: Adult retinal ganglion cell_rep1 [non-dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_M1


title: Nucleus Slc32a1-Cre:H2BG Vg_L23


title: CDLS1-3-MEGs; rep 3


title: CDLS2-1-MEGs; rep 1


title: Nucleus Slc32a1-Cre:H2BG Vg_L21


title: Adult retinal ganglion cell_rep11 [dissociated RGC]

description:
cDNA
Gene expression data from a single mouse retinal ganglion cell.
Parvalbumin-cre mice (129P2/OlaHsd) and Tomato mice (Ai9 at Jackson) (C57BL/6 and 129 SV) were mated to produce the isolated cells.

hyb_protocol: Amplified cDNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using standard Affymetrix protocols at the GeneChip Facility at Iowa State University.

scan_protocol: Affymetrix Mouse Genome 430 2.0 arrays were scanned using standard protocols at the GeneChip Facility at Iowa State University.

growth_protocol: Adult retinas were dissected and dissociated with papain at different timepoints. There was no culture or time for growth.

extract_protocol: Individual mouse retinal cells were harvested using a pulled glass pipette and were expelled into cold lysis buffer. The total single cell RNA was reverse transcribed using Superscript III combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Single cells were isolated based on their red fluorescence and immediately placed into cell lysis buffer.

value: mixed

value: dissociated retina


title: CDLS1-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_L20

value: untreated


title: Adult retinal ganglion cell_rep13 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L19


title: CDLS1-1-MEGs; rep 1


title: Adult retinal ganglion cell_rep12 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L17


title: Nucleus Slc32a1-Cre:H2BG Vg_L18


title: WT4-3-MEGs; rep 3

value: CTRL


title: Adult retinal ganglion cell_rep14 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L16


title: Adult retinal ganglion cell_rep10 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L15


title: Adult retinal ganglion cell_rep10 [non-dissociated RGC]

value: retina

value: On Orientation Selective (horizontal)


title: Adult retinal ganglion cell_rep9 [dissociated RGC]

value: retinal ganglion

value: adult


title: Nucleus Slc32a1-Cre:H2BG Vg_L22


title: Nucleus Slc32a1-Cre:H2BG Vg_L14


title: WT4-1-MEGs; rep 1


title: WT4-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_L12


title: Nucleus Slc32a1-Cre:H2BG Vg_L11


title: Adult retinal ganglion cell_rep8 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L13


title: Nucleus Slc32a1-Cre:H2BG Vg_L10


title: Nucleus Slc32a1-Cre:H2BG Vg_L8


title: Nucleus Slc32a1-Cre:H2BG Vg_L9


title: WT3-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_L7


title: Adult retinal ganglion cell_rep6 [dissociated RGC]


title: Adult retinal ganglion cell_rep5 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L6


title: Adult retinal ganglion cell_rep7 [dissociated RGC]


title: WT3-1-MEGs; rep 1


title: WT3-3-MEGs; rep 3


title: WT2-3-MEGs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_L4


title: Nucleus Slc32a1-Cre:H2BG Vg_L5


title: Adult retinal ganglion cell_rep3 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_L2


title: Nucleus Slc32a1-Cre:H2BG Vg_L1


title: WT2-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_K24


title: Nucleus Slc32a1-Cre:H2BG Vg_L3


title: WT2-1-MEGs; rep 1


title: P12_Ascl1_ChIPseq

city: Seattle

first: Thomas

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structures

institute: University of Washington

data_processing:
Sequence reads (36 bp) were mapped to the mouse mm9 genome using bwa (v 0.7.12-r1039).  Merging and sorting of sequencing reads from different lanes was performed with SAMtools (v1.2). The HOMER software suite was used to determine and score peak calls (‘findPeaks’ function, v4.7) as well as motif enrichment (‘findMotifs’ function, v4.7, using repeat mask). For STATi and control Ascl1 ChIP-seq, reads were aligned to the mm10 genome using Bowtie2. The .sam files were converted to sorted .bam files using SAMtools. MACS2 was used to call peaks with default settings using the broad peaks annotation. Peak overlap analyses were performed using Bedops. The control Ascl1 ChIP-seq .bam file was downsampled by a factor of 0.69 to normalize the number of mapped reads over the common peaks found between treatment and control samples. This downsampled .bam file was used for all analyses. Differential accessibility analysis in Ascl1 ChIP-seq peaks was determined using edgeR as detailed in the edgeR user guide.
genome build: mm9

source_name: Cultured Müller glia

extract_protocol: P0 retinas or cultured, post-natal day 12, Müller glia (+/- Ascl1 overexpression, rtTA germline:tetO-Ascl1-ires-GFP mice ± doxycycline) were digested with papain/DNase to single cells and fixed with 0.75 % formaldehyde for 10 minutes at room temperature.  Sonication was performed with a probe sonicator (Fisher Scientific): 12 pulses, 100 J/pulse, Amplitude: 45, 45 seconds cooling at 4 ºC between pulses.  Immunoprecipitation performed with 40 mL anti-mouse IgG magnetic beads (Invitrogen Cat: 110.31) and 4 mg mouse anti-MASH1 antibody (BD Pharmingen Cat: 556604) against chromatin from 5 million cells per condition according to Diagenode LowCell Number Kit using IP and Wash buffers as described in28. Libraries were prepared with standard Illumina adaptors and sequenced to an approximate depth of 36 million reads each.  Sequence reads (36 bp) were mapped to the mouse mm9 genome using bwa (v 0.7.12-r1039).

value: Post-natal day 12


title: P0_Ascl1_ChIPseq

source_name: whole retina

value: Post-natal day 0


title: Adult retinal ganglion cell_rep2 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_K23


title: STATi_Ascl1_ChIPseq

data_processing:
Sequence reads (36 bp) were mapped to the mouse mm9 genome using bwa (v 0.7.12-r1039).  Merging and sorting of sequencing reads from different lanes was performed with SAMtools (v1.2). The HOMER software suite was used to determine and score peak calls (‘findPeaks’ function, v4.7) as well as motif enrichment (‘findMotifs’ function, v4.7, using repeat mask). For STATi and control Ascl1 ChIP-seq, reads were aligned to the mm10 genome using Bowtie2. The .sam files were converted to sorted .bam files using SAMtools. MACS2 was used to call peaks with default settings using the broad peaks annotation. Peak overlap analyses were performed using Bedops. The control Ascl1 ChIP-seq .bam file was downsampled by a factor of 0.69 to normalize the number of mapped reads over the common peaks found between treatment and control samples. This downsampled .bam file was used for all analyses. Differential accessibility analysis in Ascl1 ChIP-seq peaks was determined using edgeR as detailed in the edgeR user guide.
genome build: mm10


title: WT1-3-MEGs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_K22


title: Adult retinal ganglion cell_rep4 [dissociated RGC]


title: Nucleus Slc32a1-Cre:H2BG Vg_K21


title: Adult retinal ganglion cell_rep1 [dissociated RGC]


title: Control_Ascl1_ChIPseq


title: Nucleus Slc32a1-Cre:H2BG Vg_K20


title: WT1-2-MEGs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_K19